[chimerax-users] Surfaces & color by attribute

[Elaine Meng]

I’m glad you found a solution!

Ah yes, for completeness I should have mentioned that ChimeraX does have coloring by map value (volume data, values on a 3D grid).  For example, you could color a surface by electrostatic potential (ESP) if you created an ESP map file using another program and then opened it in ChimeraX.  The “mlp” command mentioned by Tom automatically calculates a “lipophilic potential” map and then uses it for coloring.

Coloring by map value:
<http://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#map>

Elaine

> On Mar 6, 2018, at 11:27 AM, Hernando J Sosa <hernando.sosa at einstein.yu.edu> wrote:
> 
> Thanks this would work.  I also tried the  chimera workarounds to display surfaces of problematic molecules and found that  changing the vdw radii
> vdwdefine  +.01
> as suggested  solved the problem. The graphics and lighting of chimeraX  are  nicer though.
>  
> Thanks
>  
> Hernando
>  
>  
> From: Tom Goddard [mailto:goddard at sonic.net] 
> Sent: Tuesday, March 06, 2018 1:01 PM
> To: chimerax-users at cgl.ucsf.edu
> Cc: Hernando J Sosa
> Subject: Re: [chimerax-users] Surfaces & color by attribute
>  
> Hi Hernando,
>  
>   Although we don’t have the general color by attribute capability in ChimeraX yet, there is hydrophobicity surface coloring using the ChimeraX “mlp”  command (molecular lipophilicity potential).  For example,
>  
>             open 1bxw
>             mlp
>  
> Documentation
>  
>             https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/mlp.html
>  
> The PDB uses ChimeraX mlp for hydrophobicity images on their structure web pages, for example 1BXW image from the PDB web site below.
>  
>   http://www.rcsb.org/structure/1BXW
>  
>             Tom
>  
> On Mar 6, 2018, at 8:12 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
>  
> Hi Hernando,
> As mentioned in a recent post and also in the “Missing Features” on the download page, ChimeraX does not yet have coloring by attribute value, sorry.
> 
> <http://www.rbvi.ucsf.edu/chimerax/download.html>
> <http://plato.cgl.ucsf.edu/pipermail/chimerax-users/2018-February/000212.html>
> 
> In Chimera you could try making a molmap surface, coloring the atoms under that surface by attribute, and then using Color Zone to color the surface to match the nearby atoms.  See #3 in the surface workarounds page:
> 
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/surfprobs.html>
> 
> I hope this helps,
> Elaine
> 
> On Mar 6, 2018, at 6:10 AM, Hernando J Sosa <hernando.sosa at einstein.yu.edu> wrote:
> 
> Dear ChimeraX
> Is it possible to color a surface by  atom/residue attribute (hydrohobicity, charge)?  I know it is possible to do it in ucsf-chimera but unfortunately  surface calculation does not work in chimera  for the files I am working on. 
> Thanks
> Hernando
>